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Yorodumi- PDB-1ro9: CRYSTAL STRUCTURES OF THE CATALYTIC DOMAIN OF PHOSPHODIESTERASE 4... -
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-Basic information
Entry | Database: PDB / ID: 1ro9 | ||||||
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Title | CRYSTAL STRUCTURES OF THE CATALYTIC DOMAIN OF PHOSPHODIESTERASE 4B2B COMPLEXED WITH 8-Br-AMP | ||||||
Components | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | ||||||
Keywords | HYDROLASE / PDE / 8-Br-AMP | ||||||
Function / homology | Function and homology information negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / gamma-tubulin complex / negative regulation of relaxation of cardiac muscle / 3',5'-cyclic-AMP phosphodiesterase / neutrophil homeostasis / regulation of cardiac muscle cell contraction / gamma-tubulin binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / leukocyte migration / voltage-gated calcium channel complex ...negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / gamma-tubulin complex / negative regulation of relaxation of cardiac muscle / 3',5'-cyclic-AMP phosphodiesterase / neutrophil homeostasis / regulation of cardiac muscle cell contraction / gamma-tubulin binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / leukocyte migration / voltage-gated calcium channel complex / cAMP catabolic process / calcium channel regulator activity / excitatory synapse / 3',5'-cyclic-AMP phosphodiesterase activity / DARPP-32 events / cAMP binding / cellular response to epinephrine stimulus / positive regulation of interleukin-2 production / neutrophil chemotaxis / Z disc / positive regulation of type II interferon production / synaptic vesicle / cellular response to xenobiotic stimulus / T cell receptor signaling pathway / cellular response to lipopolysaccharide / transmembrane transporter binding / dendritic spine / postsynaptic density / centrosome / perinuclear region of cytoplasm / signal transduction / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Xu, R.X. / Rocque, W.J. / Lambert, M.H. / Vanderwall, D.E. / Nolte, R.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structures of the catalytic domain of phosphodiesterase 4B complexed with AMP, 8-Br-AMP, and rolipram. Authors: Xu, R.X. / Rocque, W.J. / Lambert, M.H. / Vanderwall, D.E. / Luther, M.A. / Nolte, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ro9.cif.gz | 153.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ro9.ent.gz | 120.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ro9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/1ro9 ftp://data.pdbj.org/pub/pdb/validation_reports/ro/1ro9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43451.852 Da / Num. of mol.: 2 / Fragment: catalytic domain / Mutation: S487A, S489A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4B / Production host: unidentified baculovirus References: UniProt: Q07343, 3',5'-cyclic-nucleotide phosphodiesterase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 3000, sodium acetate, glycerol, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 12, 1999 |
Radiation | Monochromator: monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→20 Å / Num. all: 50771 / Num. obs: 47915 / % possible obs: 94.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.13→2.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3 / Num. unique all: 9415 / Rsym value: 0.492 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: catalytic domain of holo PDE4B2B Resolution: 2.13→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
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Solvent computation | Solvent model: MASK | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→20 Å
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Refine LS restraints |
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